Apps for IGB

From Loraine Lab and Community Contributors

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Search InterPro and display motifs on gene models
100.0 232 Downloads | Citations
Version: 9.1.3


ProtAnnot is an IGB App that displays protein annotations next to gene models, making it easy to see how alternative splicing, alternative promoters, and alternative polyadenylation change gene function.

ProtAnnot is developed in the Genome Visualization Lab, part of the College of Computing and Informatics at University of North Carolina at Charlotte.

Install ProtAnnot

Use the IGB App Store or the IGB App Manager to install ProtAnnot into IGB.

Start ProtAnnot from IGB

Once ProtAnnot is installed, you can open ProtAnnot in IGB by selecting one or more gene models on the same strand of DNA and selecting Tools > Start ProtAnnot.

A new window will then open, showing the same gene models you selected.

Using ProtAnnot

Gene models will look the same as in IGB, except that exons will be color-coded according to their frame of translation. ProtAnnot shows the same reference sequence as IGB but numbers the base pair positions starting from the beginning of the gene, not the start of the chromosome as with IGB.

In addition to the gene models, ProtAnnot shows an exon summary graphic at the bottom of the display that summarizes the number of gene models that have sequence at each position along the axis. (It's like a coverage graph, but for gene models.)

In ProtAnnot, you can zoom and scroll the same as in IGB.

To run a search, click the Interpro tab and go from there.

Once a search finishes, ProtAnnot will display the results as green bars next to the gene models. ProtAnnot will also display a link to the XML output files from InterPro.

You can save the results. Just use the File menu to save your data to a file. Later on, you can open the file without needing to select gene models in the main IGB window.

More more info

For more information about ProtAnnot, including an example gene with an interesting alternative splicing pattern, see the ProtAnnot paper:

ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins

Current Version : 9.1.3

Release Date : 8 Jul, 2020

Works with IGB 9.1.0+

Version : 9.1.2

Release Date : 21 Mar, 2020

Works with IGB 9.1.0+

Version : 9.1.0

Release Date : 20 Dec, 2019

Works with IGB 9.1.0+

To install and run this App, start IGB! Then come back and refresh this page.

App Version 9.1.3
Works with IGB 9.1.0+